A time-resolved clonogenic assay for improved cell survival and RBE measurements.

Purpose: The in vitro clonogenic assay (IVCA) is the mainstay of quantitative radiobiology. Here, we investigate the benefit of a time-resolved IVCA version (trIVCA) to improve the quantification of clonogenic survival and relative biological effectiveness (RBE) by analyzing cell colony growth behavior. Materials & Methods: In the IVCA, clonogenicity classification of cell colonies is performed based on a fixed colony size threshold after incubation. In contrast, using trIVCA, we acquire time-lapse microscopy images during incubation and track the growth of each colony using neural-net-based image segmentation. Attributes of the resulting growth curves are then used as predictors for a decision tree classifier to determine clonogenicity of each colony. The method was applied to three cell lines, each irradiated with 250 kV X-rays in the range 0-8 Gy and carbon ions of high LET (100 keV/µm, dose-averaged) in the range 0-2 Gy. We compared the cell survival curves determined by trIVCA to those from the classical IVCA across different size thresholds and incubation times. Further, we investigated the impact of the assaying method on RBE determination. Results: Size distributions of abortive and clonogenic colonies overlap consistently, rendering perfect separation via size threshold unfeasible at any readout time. This effect is dose-dependent, systematically inflating the steepness and curvature of cell survival curves. Consequently, resulting cell survival estimates show variability between 3% and 105%. This uncertainty propagates into RBE calculation with variability between 8% and 25% at 2 Gy.Determining clonogenicity based on growth curves has an accuracy of 95% on average. Conclusion: The IVCA suffers from substantial uncertainty caused by the overlap of size distributions of delayed abortive and clonogenic colonies. This impairs precise quantification of cell survival and RBE. By considering colony growth over time, our method improves assaying clonogenicity.

Iatrogenic influence on prognosis of radiation-induced contrast enhancements in patients with glioma WHO 1-3 following photon and proton radiotherapy.

BACKGROUND AND PURPOSE: Radiation-induced contrast enhancements (RICE) are a common side effect following radiotherapy for glioma, but both diagnosis and handling are challenging. Due to the potential risks associated with RICE and its challenges in differentiating RICE from tumor progression, it is critical to better understand how RICE prognosis depends on iatrogenic influence. MATERIALS AND METHODS: We identified 99 patients diagnosed with RICE who were previously treated with either photon or proton therapy for World Health Organization (WHO) grade 1-3 primary gliomas. Post-treatment brain MRI-based volumetric analysis and clinical data collection was performed at multiple time points. RESULTS: The most common histologic subtypes were astrocytoma (50%) and oligodendroglioma (46%). In 67%, it was graded WHO grade 2 and in 86% an IDH mutation was present. RICE first occurred after 16 months (range: 1-160) in median. At initial RICE occurrence, 39% were misinterpreted as tumor progression. A tumor-specific therapy including chemotherapy or re-irradiation led to a RICE size progression in 86% and 92% of cases, respectively and RICE symptom progression in 57% and 65% of cases, respectively. A RICE-specific therapy such as corticosteroids or Bevacizumab for larger or symptomatic RICE led to a RICE size regression in 81% of cases with symptom stability or regression in 62% of cases. CONCLUSIONS: While with chemotherapy and re-irradiation a RICE progression was frequently observed, anti-edematous or anti-VEGF treatment frequently went along with a RICE regression. For RICE, correct diagnosis and treatment decisions are challenging and critical and should be made interdisciplinarily.

Radiation-induced contrast enhancement following proton radiotherapy for low-grade glioma depends on tumor characteristics and is rarer in children than adults.

BACKGROUND AND PURPOSE: Proton beam radiotherapy (PRT) is used in the treatment of low-grade glioma (LGG) to mitigate long-term sequelae. Following PRT, increased rates of radiation-induced contrast enhancements (RICE) are suspected but poorly understood. MATERIALS AND METHODS: We analyzed consecutive 227 patients (42 children and 185 adults) treated with PRT (54 Gy RBE) for LGG from 2010 to 2020 and followed with serial clinical exams and magnetic resonance imaging for in median 5.6 years. RESULTS: Tumors were graded WHO 1 in a minority (n = 22, 12%) of adults, but a majority of children (n = 29, 69%). In contrast, tumors were graded WHO 2 in the majority (n = 160, 87%) of adults and a minority of children (n = 10, 24%). Five-year overall survival following PRT was 81% in adults and 91% in children. The risk of RICE was 5-fold more frequent in adults (25%) vs. children (5%; p = 0.0043). In children and adults, RICE were symptomatic in 50% and 55% (n = 1 and 26) of cases with CTCAE grade 0 in 47% (n = 23), grade 1 in 25% (n = 12), 0% grade 2 (n = 0) and 29% grade 3 (n = 14), respectively. In adults, RICE risk was associated to WHO grading (8% in WHO grade 1 vs. 24% in WHO grade 2, p = 0.026), independent of age (p = 0.44) and irradiation dose (p = 0.005), but not independent of IDH mutational status. CONCLUSIONS: These data demonstrate effectiveness of PRT for LGG in both children and adults. The RICE risk is lower in children which are a main target group for PRT and differs with WHO grading.

VisuStatR: visualizing motility and morphology statistics on images in R.

MOTIVATION: Live-cell microscopy has become an essential tool for analyzing dynamic processes in various biological applications. Thereby, high-throughput and automated tracking analyses allow the simultaneous evaluation of large numbers of objects. However, to critically assess the influence of individual objects on calculated summary statistics, and to detect heterogeneous dynamics or possible artifacts, such as misclassified or -tracked objects, a direct mapping of gained statistical information onto the actual image data would be necessary. RESULTS: We present VisuStatR as a platform independent software package that allows the direct visualization of time-resolved summary statistics of morphological characteristics or motility dynamics onto raw images. The software contains several display modes to compare user-defined summary statistics and the underlying image data in various levels of detail. AVAILABILITY AND IMPLEMENTATION: VisuStatR is a free and open-source R-package, containing a user-friendly graphical-user interface and is available via GitHub at https://github.com/grrchrr/VisuStatR/ under the MIT+ license. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Radiation induced contrast enhancement after proton beam therapy in patients with low grade glioma - How safe are protons?

PURPOSE: The optimal treatment strategy for low-grade glioma (LGG) is still a matter of controversy. Considering that the prognosis is typically favorable, the prevention of late sequelae is of particular importance. Proton beam therapy (PRT) has the potential to further reduce the burden of treatment related side effects. We set out to evaluate the clinical outcome of proton irradiation with a particular focus on morphologic features on magnetic resonance imaging (MRI). METHODS: We assessed prospectively 110 patients who received radiotherapy with protons for histologically proven LGG. Clinical and radiological information were analyzed resulting in more than 1200 available MRI examinations with a median follow-up of 39 months. Newly diagnosed contrast-enhancing lesions on MRI were delineated and correlated with parameters of the corresponding treatment plan. A voxel-based dose-matched paired analysis of the linear energy transfer (LET) inside vs outside lesions was performed. RESULTS: Proton beam irradiation of patients with low-grade glioma results in overall survival (OS) of 90% after seven years. Median progression free survival had not yet been reached with surviving fraction of 54% after seven years. The incidence of temporary or clinically silent radiation induced contrast enhancement was significantly higher than previously assumed, however, symptomatic radiation necrosis was only detected in one patient. These radiation-induced contrast-enhancing lesions were almost exclusively seen at the distal beam end of the proton beam. In 22 out of 23 patients, the average LET of voxels inside contrast-enhancing lesions was significantly increased, compared to dose-matched voxels outside the lesions. CONCLUSION: Symptomatic radiation necrosis following PRT was as rare as conventional photon-based treatment series suggest. However, the increased incidence of asymptomatic radiation-induced brain injuries with an increased average LET observed in this cohort provides strong clinical evidence to support the hypothesis that the relative biological effectiveness of protons is variable and different to the fixed factor of 1.1 currently used worldwide.

Models for Translational Proton Radiobiology-From Bench to Bedside and Back.

The number of proton therapy centers worldwide are increasing steadily, with more than two million cancer patients treated so far. Despite this development, pending questions on proton radiobiology still call for basic and translational preclinical research. Open issues are the on-going discussion on an energy-dependent varying proton RBE (relative biological effectiveness), a better characterization of normal tissue side effects and combination treatments with drugs originally developed for photon therapy. At the same time, novel possibilities arise, such as radioimmunotherapy, and new proton therapy schemata, such as FLASH irradiation and proton mini-beams. The study of those aspects demands for radiobiological models at different stages along the translational chain, allowing the investigation of mechanisms from the molecular level to whole organisms. Focusing on the challenges and specifics of proton research, this review summarizes the different available models, ranging from in vitro systems to animal studies of increasing complexity as well as complementing in silico approaches.

Motion of water monomers reveals a kinetic barrier to ice nucleation on graphene.

The interfacial behaviour of water remains a central question to fields as diverse as protein folding, friction and ice formation. While the properties of water at interfaces differ from those in the bulk, major gaps in our knowledge limit our understanding at the molecular level. Information concerning the microscopic motion of water comes mostly from computation and, on an atomic scale, is largely unexplored by experiment. Here, we provide a detailed insight into the behaviour of water monomers on a graphene surface. The motion displays remarkably strong signatures of cooperative behaviour due to repulsive forces between the monomers, enhancing the monomer lifetime ( ≈ 3 s at 125 K) in a free-gas phase that precedes the nucleation of ice islands and, in turn, provides the opportunity for our experiments to be performed. Our results give a molecular perspective on a kinetic barrier to ice nucleation, providing routes to understand and control the processes involved in ice formation.

How can scanned proton beam treatment planning for low-grade glioma cope with increased distal RBE and locally increased radiosensitivity for late MR-detected brain lesions?

A novel risk model has recently been proposed for the occurrence of late contrast-enhancing brain lesions (CEBLs) after proton irradiation of low-grade glioma (LGG) patients. It predicts a strong dependence on dose-weighted linear-energy transfer (LETd effect) and an increased radiosensitivity of the ventricular proximity, a 4-mm fringe surrounding the ventricular system (VP4mm effect). On this basis, we investigated (A) how these two risk factors and patient-specific anatomical and treatment plan (TP) features contribute to normal tissue complication probability (NTCP) and (B) if conventional LETd -reduction techniques like multiple-field TP are able to reduce NTCP. (A) The LGG model cohort (N = 110) was stratified with respect to prescribed dose, tumor grade, and treatment field configuration. NTCP predictions and CEBL occurrence rates per strata were analyzed. (B) The effect of multiple-field TP was investigated in two patient groups: (i) nine high-risk subjects with extended lateral target volumes who had developed CEBLs after single-beam treatments were retrospectively replanned with a clinical standard two-field setting using almost orthogonal fields and strictly opposing fields, (ii) single-field treatments were simulated for seven low-risk patients with small central target volumes clinically treated with two strictly opposing fields. (A) In the model cohort, we identified the exposure of the radiosensitive VP4mm fringe with proton field components of increased biological effectiveness as dominant NTCP driving factor. We observed that larger target volumes and location lateral to the main ventricles, both being characteristic for WHO°II tumors, presented with the highest complication risks. Among subjects of an equal dose prescription of 54 Gy(RBE), the highest median NTCP was obtained for the WHO°II group treated with two fields using sharp angles. (B) Regarding the effect of multiple-field plans, we found that an NTCP reduction was only achievable in the low-risk group where the LETd effect dominates and the VP4mm effect is small. NTCP of the single-field plans was 23% higher compared to the clinical opposing field plan. In the high-risk group, where the VP4mm effect dominates the risk, both two-field scenarios yielded 44% higher NTCP predictions compared to the clinical single-field plans. The interplay of an increased radiosensitivity in the VP4mm fringe with proton field components of increased biological effectiveness creates a geometric complexity that can hardly be managed by current clinical TP. Our results underline that advanced biologically guided TP approaches become crucial for an effective risk minimization in proton therapy of LGG.

Inter-adsorbate forces and coherent scattering in helium spin-echo experiments.

In studies of dynamical systems, helium atoms scatter coherently from an ensemble of adsorbates as they diffuse on the surface. The results give information on the co-operative behaviour of interacting adsorbates and thus include the effects of both adsorbate-substrate and adsorbate-adsorbate interactions. Here, we discuss a method to disentangle the effects of interactions between adsorbates from those with the substrate. The result gives an approximation to observations that would be obtained if the scattering was incoherent. Information from the experiment can therefore be used to distinguish more clearly between long-range inter-adsorbate forces and the short range effects arising from the local lattice potential and associated thermal excitations. The method is discussed in the context of a system with strong inter-adsorbate interactions, sodium atoms diffusing on a copper (111) surface.

A framework for automated time-resolved analysis of cell colony growth after irradiation.

Understanding dose-dependent survival of irradiated cells is a pivotal goal in radiotherapy and radiobiology. To this end, the clonogenic assay is the standard in vitro method, classifying colonies into either clonogenic or non-clonogenic based on a size threshold at a fixed time. Here we developed a methodological framework for the automated analysis of time course live-cell image data to examine in detail the growth dynamics of large numbers of colonies that occur during such an experiment. We developed a segmentation procedure that exploits the characteristic composition of phase-contrast images to identify individual colonies. Colony tracking allowed us to characterize colony growth dynamics as a function of dose by extracting essential information: (a) colony size distributions across time; (b) fractions of differential growth behavior; and (c) distributions of colony growth rates across all tested doses. We analyzed three data sets from two cell lines (H3122 and RENCA) and made consistent observations in line with already published results: (i) colony growth rates are normally distributed with a large variance; (ii) with increasing dose, the fraction of exponentially growing colonies decreases, whereas the fraction of delayed abortive colonies increases; as a novel finding, we observed that (iii) mean exponential growth rates decrease linearly with increasing dose across the tested range (0-10 Gy). The presented method is a powerful tool to examine live colony growth on a large scale and will help to deepen our understanding of the dynamic, stochastic processes underlying the radiation response in vitro.

Volume-dependent dose-response of the intestinal stem cell niche and lymphoid tissue.

BACKGROUND AND PURPOSE: Plasticity of the intestinal stem cell compartment in response to radiation injury is regulated by a stem cell niche. We present here the first experimental observations of a dose-volume effect of the intestinal stem cell niche and of the solitary intestinal lymphoid tissues (SILT). MATERIALS AND METHODS: Regeneration of intestinal crypts in mice was studied following irradiation of millimetre-size jejunal sections with single doses of 6 to 24 Gy and compared to total body irradiation (TBI). The statistical distribution of cells per crypt was scored and regressed to a biomathematical model. The number of SILTs was scored for different doses and field sizes and crypt regeneration was correlated with SILT proximity. RESULTS: We observed a differential dose-response of the intestinal stem cell niche at the centres of the irradiated sections, but only for field sizes below 10 mm. Irradiation of 5 mm jejunum results in an increase in crypt survival by up to an order of magnitude, compared to TBI. Distributions of cell-per-crypt numbers and comparison to biomathematical modelling suggest that these observations stem from a field size-dependent regeneration rate. The density of SILTs also exhibits a volume-dependent dose-response and increased crypt survival correlates with a proximity to SILTs. CONCLUSION: Our findings present the first observation of a field-size dependent dose-response of the intestinal stem cell niche. Its regeneration process does apparently not rely on distant radiation-sensitive resources of the organism, such as the bone marrow. Yet, our observations suggest that the niche interacts with intact tissue in millimetres distance, leading to faster crypt regeneration. The field-size dependent dose-response of SILTs posits a role of the immune system on the dose-volume effect.

Late Contrast Enhancing Brain Lesions in Proton-Treated Patients With Low-Grade Glioma: Clinical Evidence for Increased Periventricular Sensitivity and Variable RBE.

PURPOSE: Late radiation-induced contrast-enhancing brain lesions (CEBLs) on magnetic resonance imaging (MRI) after proton therapy of brain tumors have been observed to occur frequently in regions of high linear energy transfer (LET) and in proximity to the ventricular system. We analyzed 110 patients with low-grade glioma treated with proton therapy to determine whether the risk for CEBLs is increased in proximity to the ventricular system and if there is a relationship between relative biological effectiveness (RBE) and LET. METHODS AND MATERIALS: We contoured CEBLs identified on follow-up T1-MRI scans and computed dose and dose-averaged LET (LETd) distributions for all patients using the Monte Carlo method. We then performed cross-validated voxel-level logistic regression to predict local risks for image change and to extract model parameters, such as the RBE. From the voxel-level model, we derived a model for patient-level risk prediction based on the treatment plan. RESULTS: Of 110 patients, 23 exhibited 1 or several CEBLs on follow-up MRI scans. The voxel-level logistic model has an accuracy as follows: area under the curve of 0.94 and Brier score of 2.6 × 10-5. Model predictions are a 3-fold increased risk in the 4 mm region around the ventricular system and an LETd-dependent RBE of, for example, 1.20 for LETd = 2 keV/µm and 1.50 for LETd = 5 keV/µm. The patient-level risk model has an accuracy as follows: area under the curve of 0.78 and Brier score of 0.13. CONCLUSIONS: Our findings present clinical evidence for an increased risk in ventricular proximity and for a proton RBE that increases significantly with increasing LET. We present a voxel-level model that accurately predicts the localization of late MRI contrast change and extrapolate a patient-level model that allows treatment plan-based risk prediction.

On the limitations of the area under the ROC curve for NTCP modelling.

The area under the ROC curve (AUC) is commonly used as a measure for the discriminative performance of NTCP models. Here, we demonstrate that for typical patient cohorts, the AUC is an unsuitable measure for that purpose since it is typically limited to values below 0.8 and it exhibits large statistical variation.

Reserve stem cell population in intestinal crypts found to be consistently small by analysis of in vivo clonogenic assays with a biomathematical dynamic model.

BACKGROUND AND PURPOSE: The high plasticity of the intestinal epithelium is maintained by a resilient reserve stem cell population, whose extent and biology are a matter of ongoing debate. The in vivo clonogenic assay (IVCA), presents a well established and efficient analysis of radiation insult to the intestinal crypts. However, we found that inadequate mathematical analysis over the last four decades led to systematic errors and contradictory results in estimates of radio-sensitivity and size of the reserve stem cell pool. MATERIAL AND METHODS: We devised a refinement of the IVCA via development of a biomathematical model that delivers a full statistical dynamic description of epithelial radiation injury and subsequent regeneration. We validated the model against cellular and crypt distribution statistics obtained from IVCA experiments and through systematic re-analysis of experimental data from 27 publications. RESULTS: A full dynamic description of the evolution of stem cell niche population statistics is obtained. A systematic re-analysis reveals a consistent clonogenic content of the crypt of 31±6 cells. The stem cell reserve manifests to be, contrary to prior predictions, radio-resistant: α=(0.22±0.04) Gy-1. CONCLUSION: We established a precision tool for the quantitative analysis of radiation insult to the intestinal crypts, which we employ to show that the reserve stem cell population is small, radio-resistant, and remarkably immutable against a large variety of interventions. The increased resolution of the model allows not only a reduction of the number of animals by about 75%, but also to quantify experimentally the influence of additional agents on damage and on regeneration of the stem cell niche.

Ballistic Diffusion in Polyaromatic Hydrocarbons on Graphite.

This work presents an experimental picture of molecular ballistic diffusion on a surface, a process that is difficult to pinpoint because it generally occurs on very short length scales. By combining neutron time-of-flight data with molecular dynamics simulations and density functional theory calculations, we provide a complete description of the ballistic translations and rotations of a polyaromatic hydrocarbon (PAH) adsorbed on the basal plane of graphite. Pyrene, C16H10, adsorbed on graphite is a unique system, where at relative surface coverages of about 10-20% its mean free path matches the experimentally accessible time/space scale of neutron time-of-flight spectroscopy (IN6 at the Institut Laue-Langevin). The comparison between the diffusive behavior of large and small PAHs such as pyrene and benzene adsorbed on graphite brings a strong experimental indication that the interaction between molecules is the dominating mechanism in the surface diffusion of polyaromatic hydrocarbons adsorbed on graphite.

Graphene on Ni(111): Electronic Corrugation and Dynamics from Helium Atom Scattering.

Using helium atom scattering, we have studied the structure and dynamics of a graphene layer prepared in situ on a Ni(111) surface. Graphene/Ni(111) exhibits a helium reflectivity of ∼20% for a thermal helium atom beam and a particularly small surface electron density corrugation ((0.06 ± 0.02) Å peak to peak height). The Debye-Waller attenuation of the elastic diffraction peaks of graphene/Ni(111) and Ni(111) was measured at surface temperatures between 150 and 740 K. A surface Debye temperature of θD = (784 ± 14) K is determined for the graphene/Ni(111) system and θD = (388 ± 7) K for Ni(111), suggesting that the interlayer interaction between graphene and the Ni substrate is intermediary between those for strongly interacting systems like graphene/Ru(0001) and weakly interacting systems like graphene/Pt(111). In addition we present measurements of low frequency surface phonon modes on graphene/Ni(111) where the phonon modes of the Ni(111) substrate can be clearly observed. The similarity of these findings with the graphene/Ru(0001) system indicates that the bonding of graphene to a metal substrate alters the dynamic properties of the graphene surface strongly and is responsible for the high helium reflectivity of these systems.

The structure of deuterated benzene films adsorbed on the graphite (0001) basal plane: what happens below and above the monolayer coverage?

An exact description of the interactions in aromatic carbon systems is a key condition for the design of carbon based nanomaterials. In this paper we investigate the binding and adsorbate structure of the simplest prototype system in this class - the single aromatic ring molecule benzene on graphite. We have collected neutron diffraction data of the ordered phase of deuterated benzene, C6D6, adsorbed on the graphite (0001) basal plane surface. We examined relative coverages from 0.15 up to 1.3 monolayers (ML) in a temperature range of 80 to 250 K. The results confirm the flat lying commensurate (√7 × âˆš7)R19.1° monolayer with lattice constants a = b = 6.5 Å at coverages of less than 1 ML. For this structure we observe a progressive melting well below the desorption temperature. At higher coverages we do neither observe an ordered second layer nor a densification of the structure by upright tilting of first layer molecules, as generally assumed up to now. Instead, we see the formation of clusters with a bulk crystalline structure for coverages only weakly exceeding 1 ML.